Preheat oven to 375 degrees F. Spray a 12-cup muffin tin with nonstick cooking spray; set aside.
In a large mixing bowl, whisk together applesauce, Truvia, pumpkin, Greek yogurt, milk and vanilla.
Mix in baking soda, baking powder, salt, pumpkin pie spice, flour and protein powder until well combined.
Fold in chocolate chips then divide batter evenly between muffin cups. Bake for 18-20 minutes, or until set.